MolNFT v1 · #174827 · protein
Crystal structure of the SARS-cov-2 main protease in complex with telaprevir
7C7P · 3C-like proteinase: “Crystal structure of the SARS-cov-2 main protease in complex with telaprevir”. X-ray diffraction, 2 ligands (SV6, CL), 8 pockets (best druggability 0.76). MolNFT v1 #174827 on GenesisL1: 3D structure, binding…
- PDB
- 7C7P
- Type
- protein
- Length
- 601 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- SV6, CL
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 301 | 27% helix, 28% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 300 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- SV6 · (1S,3aR,6aS)-2-[(2S)-2-({(2S)-2-cyclohexyl-2-[(pyrazin-2-ylcarbonyl)amino]acetyl}amino)-3,3-dimethylbutanoyl]-N-[(2R,3S)-1-(cyclopropylamino)-2-hydroxy-1-oxohexan-3-yl]octahydrocyclopenta[c]pyrrole-1-carboxamide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 873 | 0.76 | 0.80 | 76 | CL |
| 2 | 459 | 0.61 | 0.75 | 61 | empty |
| 3 | 214 | 0.48 | 0.75 | 30 | SV6 |
| 4 | 172 | 0.43 | 0.74 | 27 | SV6 |
| 5 | 130 | 0.41 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1498 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7C7P · Crystal structure of the SARS-CoV-2 main protease in complex with Telaprevir · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0DTD1
- Elsewhere: RCSB PDB 7C7P · PDBe 7C7P · UniProt P0DTD1
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